Additional file 3 of A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset
dataset
posted on 2024-08-14, 19:48 authored by Yong Zhou, Nagarajan Kathiresan, Zhichao Yu, Luis F. Rivera, Yujian Yang, Manjula Thimma, Keerthana Manickam, Dmytro Chebotarov, Ramil Mauleon, Kapeel Chougule, Sharon Wei, Tingting Gao, Carl D. Green, Andrea Zuccolo, Weibo Xie, Doreen Ware, Jianwei Zhang, Kenneth L. McNally, Rod A. WingAdditional file 3: Table S1. Summary of workflow phases. Table S2. Performance of the genome variant calling workflow (w/GATK4) for rice, sorghum, maize and soybean. Table S3. Results of variant detection based on the automated workflow for rice, sorghum, maize, and soybean. Table S4. SNPEff annotations for rice, sorghum, maize, and soybean. Table S5. The number of SNPs was identified by using rice RPRP references. Table S6. Results of novel SNP annotation in genes. Table S7. Results of SNP analysis in open chromatin regions verse genome-wide regions.
